New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library (...) !
BioRuby project
14 months
30
17
66716
1441
0
0
Parser of scientific names (...) !
Dmitry Mozzherin
7 months
14
5
37014
690
0
0
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
10 weeks
14
11
30391
478
0
3
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall
4 months
4
1
30294
870
0
0
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
8 weeks
17
5
25076
620
0
57
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
3 months
2
...
20426
696
0
139
Http requests to entrez e-utilities (...)
Jared Ning
2 years
4
...
19177
255
0
0
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
4 months
13
1
19121
364
Gadgets for bioinformatics (...)
Shintaro Katayama
13 months
...
17028
464
0
0
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
6 months
30
30
15813
257
2
51
Gff3 parser for big data (...) !
Pjotr Prins
23 months
6
2
15292
209
0
0
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
4 months
...
14783
670
Maf parser for BioRuby (...)
Clayton Wheeler
24 months
10
30
13573
270
0
0
Interfaces with biomodel search engine (...) !
Niall Beard
2 years
...
12962
180
0
0
Create pretty svg-format images of features, gene models (...)
Dan MacLean
6 months
7
5
11596
450
A biogem to submit jobs on a queue (...)
Francesco Strozzi
21 months
5
...
11561
256
0
0
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
11194
148
0
0
Very fast blast xml parser and library for (...) !
Pjotr Prins
17 months
9
...
9108
161
0
0
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
8750
154
0
0
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
11 weeks
6
4
8465
175
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
8 weeks
7
20
7831
201
0
14
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
2 years
1
1
7623
107
0
0
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
17 months
1
...
7380
116
0
0
Build genome output files (...)
Michael Barton
11 months
3
...
7032
82
0
0
Low memory sequence emitters (...)
Pjotr Prins
10 weeks
8
1
6961
141
0
9
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
3 years
4
...
6762
78
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
23 months
1
...
6272
101
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
1
6259
84
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
13 months
6
...
6197
83
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
4 years
6180
54
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
20 months
2
...
6177
107
0
0
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
2 years
3
...
6047
91
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
11 months
8
3
6030
167
3
13
Data mining algorithms for jRuby (...)
arrigonialberto86
10 months
14
3
5952
226
0
0
Ruby wrapper for sambamba tool (...)
Artem Tarasov
23 months
2
...
5854
102
0
0
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
6 years
5852
66
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
14 months
5
...
5633
126
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
5622
74
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
29
14
5394
63
0
0
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
5174
67
0
0
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
3 years
8
...
4540
45
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
4452
69
0
0
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
24 months
2
...
4378
92
0
0
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
3 years
30
4
4292
33
0
0
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
4262
68
0
0
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
20 months
2
...
4081
63
Read and manipulate cd-hit clusters (...)
George Githinji
15 months
2
1
3752
88
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
3 years
1
...
3454
43
Ruby binding for samtools tabix (...)
throwern
10 months
3
...
3451
98
0
0
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
2 years
1
...
3428
43
0
0
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
24 months
3256
68
Ruby support for the baclava file format (...) !
Robert Haines
4 months
1
...
3212
526
0
0
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
3187
66
Ruby binding to the ucsc kent utilities (...)
throwern
22 months
2
...
3176
70
Next-generation mapping of mutations (...)
Dan MacLean
20 months
2
...
3162
65
0
0
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3138
47
20
77
Parse affymetrix cel/cdf files (...)
Pjotr Prins
2 years
2
1
3087
42
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
11 months
10
2
3044
120
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
2 years
1
...
2910
45
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
2728
45
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
2 years
1
...
2678
45
0
0
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
17 months
...
2412
67
Taverna player is a rails plugin to run (...)
Robert Haines
5 weeks
4
...
2395
138
0
11
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2339
40
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
14 months
...
2292
66
0
0
A protparam compatible utility for BioRuby (...)
hryk
19 months
1
...
2283
45
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
11 months
1
...
2256
70
0
0
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
10 months
...
2252
94
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
21 months
2
...
2189
47
0
0
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
3 years
4
...
1799
22
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
3 years
3
...
1784
21
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
2 years
1
1780
20
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
4 months
...
1754
519
0
0
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
4 years
1
...
1730
14
Publish scientific results to the semantic web (...) !
Will Strinz
7 weeks
3
16
1712
99
0
3
Parser to work with file formats used in (...)
Ben J Woodcroft
2 weeks
...
1548
251
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1526
24
0
0
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
2 years
1
...
1525
25
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
2 years
...
1488
28
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
2 years
2
...
1474
25
0
0
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
2 years
3
...
1469
25
0
0
One-line summary of your gem (...)
Toshiaki Katayama
2 years
1
...
1456
25
0
0
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
2 years
2
...
1428
26
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1415
25
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
2 years
1
...
1403
22
A simple biogem that allows computation of the (...)
Ben J Woodcroft
2 years
1
...
1384
24
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
2 years
1
...
1369
24
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1259
24
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
2 years
...
1238
17
0
0
Gggenome Ruby client (...)
Mitsuteru Nakao
11 months
1
...
1212
39
Build graph with jRuby (...)
Matteo Picciolini
24 months
...
1171
25
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
24 months
1
...
1168
23
Ruby ensembl rest api (...)
Alberto Donizetti
10 months
3
1
1125
45
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
4 months
...
1085
96
Generalized linear models for statsample (...)
Ankur Goel
10 months
...
1078
47
Vcf parser (...)
Pjotr Prins
5 weeks
12
6
1068
119
0
181
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
8 weeks
...
1038
122
1
23
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
18 months
...
921
23
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
6 months
...
798
46
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
6 months
...
770
51
0
0
Bio-repeatmasker (...)
Andrei Rozanski
6 months
766
54
Biostars data-mining and statistical analysis (...)
Joachim Baran
3 months
...
744
83
0
0
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
13 months
2
...
706
25
0
0
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
12 months
...
638
22
0
0
A parser for cigar format alignments (...)
Ben J Woodcroft
5 months
3
...
614
48
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
9 weeks
1
524
63
0
7
Web server for bio-samtools (...)
homonecloco
8 weeks
...
462
67
(...) pre
pre
351
2
Mine publications for gene names (...)
Pjotr Prins
5 months
...
306
26
0
0
!
Server for polymarker. to be used with cron (...) new
Ricardo H.  Ramirez-Gonzalez
1 week
...
304
304
0
13
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
4 months
2
...
252
21
0
0
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
8 weeks
...
201
39
!
Ruby inferface for kseq.h by heng li for (...) new
Fedor Gusev
2 weeks
...
117
114
0
25
(...) pre
pre
80
2
*) gem downloads (total & last 90 days) from rubygems.org as of 2014-07-31
**) number of commits on GitHub (last 7 days & last 90 days)